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Series GSE119631 Query DataSets for GSE119631
Status Public on Feb 19, 2019
Title Characterization of the dynamics of lamin A and lamin B LADs in HepG2 cells: impact of cyclosporin A
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: to qualify and quantify the rearrangement of interactions of nuclear lamins A/C and B with the genome, in relation to nuclearradial repositioning of loci and changes in gene expression, in HepG2 cells exposed to cyclosporin A. .To compare HepG2 cell line transcriptome profiling (RNA-seq) with radially positioning of the chromatin anchored at the nuclear periphery before and after CsA treatment.
Methods: To this end, we mapped lamin A and lamin B lamina-associated domains (LADs) by chromatin immunoprecipitation-sequencing (ChIP-seq) of lamin A/C (antibody sc7292x, Santa Cruz Biotechnology) and lamin B1 (antibody ab16048, Abcam), respectively. HepG2 cells were either cultured under proliferative conditions (controls) or exposed for 3 days to 10 uM cyclosporin A. We also assesed the transcriptome by RNA-seq under each condition in duplicate cultures.
Results: CsA elicits accumulation of pre-lamin A in HepG2 cells, raising the hypothesis of a global rearrangement of lamin-chromatin interactions. We show here the existence of overlapping and distinct lamin A and B lamina-associated domains (which we refer to as A- and B-LADs, respectively). Whereas B-LADs largely remain constitutive, CsA elicits the formation of facultative A-LADs. Re-localization of A-LADs occur mainly on preexisting B-LADs. However, LAD rearrangement does not correlate with systematic changes in gene expression within LADs. We find a reorganization of A- and B-LADs after CsA treatment, entailing distinct contributions of A- and B- type lamins. to genome organization. Indeed, classification of lamin A LADs and lamin B LADs into properties of ‘A-only’, ‘B-only’ and ‘A-B’ LADs show an overall loss of A-only LADs after CsA treatment. A- only and B-only LADs are highly dynamic with A-B LADs being more stable.The rearrangement of lamin association after CsA treatment correlates with repositioning of loci in the nuclear space with, notably, a loss of lamin B associated with a re-localization of loci towards the nuclear center and conversely, a gain of lamin B linked to a repositioning of loci towards the nuclear periphery. Predictions on radial repositioning of LADs, and of loci within, from 3D structural models of the genome were supported by fluorescence in situ hybridization (FISH) analyses.
Conclusions: We show that, while they amply co-localize on well-conserved LADs, lamins A and B also interact with distinct genomic regions that can interchange (switch) between lamin A and B upon CsA treatment. We unveil distinct lamin A and B interactions with chromatin, suggesting complementary contributions to genome conformation. Our data suggest that and lamins A and B may differentially modulate genome organization.
Overall design Lamin A/C and lamin B1 ChIP-seq analysis, and RNA-seq analysis, of the hepatocarcinoma HepG2 cell line under 2 different treatment conditions: control (Ctl) and cells treated with 10 µM Cyclosporin A (CsA) for 72 h. For ChIp-seq, ChIP DNA was purified by phenolchloroform extraction and ethanol precipitation, before Illumina library preparation at our sequencing facility on an Illumina HiSeq2500. For RNA-seq, total RNA was isolated from 2 replicates of control and CsA-treated cells using the RNeasy Mini Kit (Qiagen). DNase treatment was done with RQ1 RNase-Free DNase (M101, Promega) and libraries were prepared and sequenced on an Illumina HiSeq2500.
Contributor(s) Forsberg F, Brunet A, Liyakat Ali TM, Collas P
Citation(s) 30663495
Submission date Sep 07, 2018
Last update date Mar 27, 2019
Contact name Philippe Collas
Organization name University of Oslo
Department Institute of Basic Medical Sciences
Street address PO Box 1112 Blindern
City Oslo
ZIP/Postal code 0317
Country Norway
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (8)
GSM3379696 HepG2_ChipSeq_Ctrl_LMNA
GSM3379697 HepG2_ChIPSeq_Ctrl_LMNB
GSM3379698 HepG2_ChIPSeq_CsA_LMNA
BioProject PRJNA489793
SRA SRP160107

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Supplementary file Size Download File type/resource
GSE119631_RAW.tar 13.0 Mb (http)(custom) TAR (of BED, BEDGRAPH, FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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